Last updated: 2019-03-01
Checks: 4 2
Knit directory: DNASeq/
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| Name | Class | Size |
|---|---|---|
| a | packageIQR | 2.3 Kb |
| alignMerge | cwlStepParam | 306.3 Kb |
| bwa | cwlParam | 25.2 Kb |
| bwaAlign | cwlStepParam | 125.7 Kb |
| dats | packageIQR | 2.3 Kb |
| f1 | InputParam | 2.8 Kb |
| f2 | InputParam | 2.8 Kb |
| f3 | InputParam | 2.8 Kb |
| fastqc | cwlParam | 13.8 Kb |
| featureCounts | cwlParam | 19.4 Kb |
| fq2ubamJson | cwlParam | 37.4 Kb |
| GAlign | cwlStepParam | 211.9 Kb |
| geneBody_coverage | cwlParam | 21.8 Kb |
| genePredToBed | cwlParam | 16.5 Kb |
| gtfToGenePred | cwlParam | 16.5 Kb |
| hapCall | cwlStepParam | 29.6 Kb |
| hapJson | cwlParam | 19.3 Kb |
| jdCall | cwlStepParam | 129.5 Kb |
| jdJson | cwlParam | 28.3 Kb |
| markdup | cwlParam | 21.8 Kb |
| mc3 | cwlStepParam | 90.6 Kb |
| mergeBam | cwlParam | 18.4 Kb |
| mergeBamDup | cwlStepParam | 122.7 Kb |
| mvOut | cwlParam | 13.4 Kb |
| o1 | OutputParam | 2.3 Kb |
| o2 | OutputParam | 2.3 Kb |
| o2a | OutputParam | 2.3 Kb |
| o2b | OutputParam | 2.3 Kb |
| o2c | OutputParam | 2.3 Kb |
| o3 | OutputParam | 2.3 Kb |
| o4 | OutputParam | 2.4 Kb |
| o5 | OutputParam | 2.4 Kb |
| o6 | OutputParam | 2.4 Kb |
| o7 | OutputParam | 2.3 Kb |
| o8 | OutputParam | 2.3 Kb |
| p1 | InputParam | 2.8 Kb |
| p10 | InputParam | 2.8 Kb |
| p11 | InputParam | 2.8 Kb |
| p12 | InputParam | 2.8 Kb |
| p13 | InputParam | 2.8 Kb |
| p2 | InputParam | 2.8 Kb |
| p3 | InputParam | 2.8 Kb |
| p4 | InputParam | 2.8 Kb |
| p5 | InputParam | 2.8 Kb |
| p6 | InputParam | 2.8 Kb |
| p7 | InputParam | 2.8 Kb |
| p8 | InputParam | 2.8 Kb |
| p9 | InputParam | 2.8 Kb |
| read_distribution | cwlParam | 16.6 Kb |
| req1 | list | 416 bytes |
| req2 | list | 416 bytes |
| req3 | list | 416 bytes |
| rnaseq_Sf | cwlStepParam | 315.6 Kb |
| rscripts | character | 816 bytes |
| RSeQC | cwlStepParam | 126 Kb |
| runWDL | cwlParam | 21.7 Kb |
| s1 | stepParam | 19.5 Kb |
| s2 | stepParam | 44.2 Kb |
| s3 | stepParam | 20.1 Kb |
| s4 | stepParam | 19.5 Kb |
| s5 | stepParam | 28.1 Kb |
| s6 | stepParam | 133.4 Kb |
| sam2bam | cwlParam | 13.9 Kb |
| samtools_flagstat | cwlParam | 13.8 Kb |
| samtools_index | cwlParam | 14.4 Kb |
| sortBam | cwlParam | 13.8 Kb |
| STAR | cwlParam | 32.2 Kb |
| ubam2bamJson | cwlParam | 16.6 Kb |
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Untracked files:
Untracked: analysis/Rcwl_DNASeq_Align.Rmd
Untracked: analysis/Rcwl_DNASeq_Align.Rmd~
Untracked: analysis/Rcwl_GATK4.Rmd
Untracked: analysis/Rcwl_GATK4.Rmd~
Untracked: analysis/Rcwl_MC3.Rmd
Untracked: analysis/Rcwl_MC3.Rmd~
Untracked: bwaOutput.sam
Untracked: code/gatk.R
Untracked: code/gatk.R~
Untracked: data/fq1_1.fq
Untracked: data/fq1_2.fq
Untracked: data/fq2_1.fq
Untracked: data/fq2_2.fq
Untracked: data/normal.bam
Untracked: data/normal.bam.bai
Untracked: data/normal_1.fq
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Untracked: data/tumor.bam
Untracked: data/tumor.bam.bai
Untracked: data/tumor_1.fq
Untracked: data/tumor_2.fq
Untracked: file3f79542e1d70/
Untracked: output/BAM/
Untracked: output/GATK/
Untracked: output/interval.21.interval_list
Untracked: output/interval.21.intervals
Untracked: output/interval.list~
Untracked: output/interval.txt
Untracked: output/mc3/
Untracked: sample1.bam
Untracked: sample1.bam.bai
Untracked: temp/DNASeq.Rmd
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Untracked: temp/analysis/filed13439812939/
Untracked: temp/analysis/temp/
Untracked: temp/data/test.1_fastq.gz
Untracked: temp/data/test.2_fastq.gz
Untracked: temp/output/BAM/
Untracked: test.bam
Untracked: tmpl1.json
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The DNASeq alignment pipeline was included in the RcwlPipelines package. It majorly includes two steps:
Here is the short summary and step plots.
suppressPackageStartupMessages(library(Rcwl))
library(RcwlPipelines)
data("alignMerge")
short(alignMerge)
inputs:
- idBam
- RG
- threads
- Ref
- FQ1s
- FQ2s
outputs:
- oBam
- matrix
- Idx
- stat
steps:
- bwaAlign
- mergeBamDup
plotCWL(alignMerge)
plotCWL(runs(alignMerge)$bwaAlign)
plotCWL(runs(alignMerge)$mergeBamDup)
Here is an example of two samples. The “sample1” have two lanes of sequences and the “sample2” only has one pair of reads. The lists of reads1 fq1, reads2 fq2, read groups and output BAM names are defined in the inputList. The reference genome and number of threads to run the job are defined in the shared options, paramList.
fq1 <- list(sample1 = list("data/fq1_1.fq", "data/fq2_1.fq"),
sample2 = list("data/fq1_1.fq"))
fq2 <- list(sample1 = list("data/fq1_2.fq", "data/fq2_2.fq"),
sample2 = list("data/fq1_2.fq"))
rgs <- list(sample1 = list("@RG\\tID:sample1.1\\tSM:sample1", "@RG\\tID:sample1.2\\tSM:sample1"),
sample2 = list("@RG\\tID:sample2.1\\tSM:sample2"))
samples <- list(sample1 = "sample1.bam", sample2 = "sample2.bam")
inputList <- list(idBam = samples, RG= rgs, FQ1s = fq1, FQ2s = fq2)
paramList <- list(threads = 2,
Ref = "/rpcc/bioinformatics/reference/current/hs37d5.fa")
res <- runCWLBatch(alignMerge, outdir = "output/BAM",
inputList = inputList, paramList = paramList,
BPPARAM = BatchtoolsParam(workers = 2, cluster = "sge",
template = "/rpcc/bioinformatics/sge.tmpl",
resources = list(jobname="bwa",
threads = 2,
queue = "all.q")))
Outputs:
dir("output/BAM/sample1")
[1] "sample1.bam" "sample1.bam.bai" "sample1.flagstat.txt"
[4] "sample1.markdup.txt"
sessionInfo()
R version 3.5.2 Patched (2018-12-31 r75935)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.4 (Final)
Matrix products: default
BLAS: /home/qhu/usr/R-3.5/lib64/R/lib/libRblas.so
LAPACK: /home/qhu/usr/R-3.5/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] RcwlPipelines_0.99.0 testthat_2.0.1 BiocStyle_2.10.0
[4] rmarkdown_1.11 knitr_1.21 usethis_1.4.0
[7] devtools_2.0.1 Rcwl_0.99.14 S4Vectors_0.20.1
[10] BiocGenerics_0.28.0 yaml_2.2.0
loaded via a namespace (and not attached):
[1] colorspace_1.4-0 rprojroot_1.3-2 fs_1.2.6
[4] rstudioapi_0.9.0 roxygen2_6.1.1 remotes_2.0.2
[7] xml2_1.2.0 pkgload_1.0.2 jsonlite_1.6
[10] workflowr_1.2.0 shiny_1.2.0 DiagrammeR_1.0.0
[13] BiocManager_1.30.4 readr_1.3.1 compiler_3.5.2
[16] backports_1.1.3 assertthat_0.2.0 lazyeval_0.2.1
[19] cli_1.0.1 later_0.8.0 visNetwork_2.0.5
[22] htmltools_0.3.6 prettyunits_1.0.2 tools_3.5.2
[25] igraph_1.2.4 gtable_0.2.0 glue_1.3.0
[28] dplyr_0.8.0.1 batchtools_0.9.11 rappdirs_0.3.1
[31] Rcpp_1.0.0 rgexf_0.15.3 xopen_1.0.0
[34] debugme_1.1.0 xfun_0.5 stringr_1.4.0
[37] ps_1.3.0 mime_0.6 XML_3.98-1.17
[40] scales_1.0.0 hms_0.4.2 promises_1.0.1
[43] RColorBrewer_1.1-2 memoise_1.1.0 gridExtra_2.3
[46] ggplot2_3.1.0 downloader_0.4 rcmdcheck_1.3.2
[49] stringi_1.3.1 highr_0.7 Rook_1.1-1
[52] desc_1.2.0 checkmate_1.9.1 pkgbuild_1.0.2
[55] BiocParallel_1.16.6 rlang_0.3.1 pkgconfig_2.0.2
[58] commonmark_1.7 evaluate_0.13 purrr_0.3.0
[61] htmlwidgets_1.3 processx_3.2.1 tidyselect_0.2.5
[64] plyr_1.8.4 magrittr_1.5 bookdown_0.9
[67] R6_2.4.0 base64url_1.4 pillar_1.3.1
[70] withr_2.1.2 tibble_2.0.1 crayon_1.3.4
[73] viridis_0.5.1 progress_1.2.0 grid_3.5.2
[76] data.table_1.12.0 git2r_0.24.0 callr_3.1.1
[79] influenceR_0.1.0 digest_0.6.18 xtable_1.8-3
[82] tidyr_0.8.2 httpuv_1.4.5.1 brew_1.0-6
[85] munsell_0.5.0 viridisLite_0.3.0 sessioninfo_1.1.1